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Strontium in PDB 1y1h: Human Formylglycine Generating Enzyme, Oxidised Cys Refined As Hydroperoxide

Protein crystallography data

The structure of Human Formylglycine Generating Enzyme, Oxidised Cys Refined As Hydroperoxide, PDB code: 1y1h was solved by M.G.Rudolph, A.Dickmanns, R.Ficner, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.90 / 1.67
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.693, 110.334, 43.458, 90.00, 90.00, 90.00
R / Rfree (%) 14.6 / 17.6

Strontium Binding Sites:

The binding sites of Strontium atom in the Human Formylglycine Generating Enzyme, Oxidised Cys Refined As Hydroperoxide (pdb code 1y1h). This binding sites where shown within 5.0 Angstroms radius around Strontium atom.
In total 2 binding sites of Strontium where determined in the Human Formylglycine Generating Enzyme, Oxidised Cys Refined As Hydroperoxide, PDB code: 1y1h:
Jump to Strontium binding site number: 1; 2;

Strontium binding site 1 out of 2 in 1y1h

Go back to Strontium Binding Sites List in 1y1h
Strontium binding site 1 out of 2 in the Human Formylglycine Generating Enzyme, Oxidised Cys Refined As Hydroperoxide


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 1 of Human Formylglycine Generating Enzyme, Oxidised Cys Refined As Hydroperoxide within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Sr1001

b:11.3
occ:1.00
O X:ASN293 2.5 9.9 1.0
OE2 X:GLU300 2.5 10.4 1.0
O X:GLY296 2.5 9.2 1.0
O X:ALA298 2.5 8.8 1.0
OE2 X:GLU130 2.6 10.4 1.0
O X:HOH2017 2.6 12.6 1.0
O X:ILE294 2.9 12.0 1.0
CD X:GLU300 3.4 11.4 1.0
CD X:GLU130 3.6 12.1 1.0
C X:ILE294 3.6 10.5 1.0
C X:ASN293 3.7 9.3 1.0
C X:ALA298 3.7 9.7 1.0
CG X:GLU300 3.7 10.3 1.0
C X:GLY296 3.7 9.9 1.0
N X:ALA298 3.9 10.1 1.0
CG X:GLU130 4.1 8.8 1.0
CA X:ILE294 4.2 10.5 1.0
C X:VAL295 4.2 10.2 1.0
N X:GLY296 4.3 9.9 1.0
N X:VAL295 4.4 10.7 1.0
CA X:ALA298 4.4 10.0 1.0
N X:ILE294 4.4 9.5 1.0
O X:GLY332 4.4 11.7 1.0
O X:VAL295 4.5 9.8 1.0
CA X:VAL295 4.5 10.3 1.0
OE1 X:GLU300 4.5 10.8 1.0
NH2 X:ARG364 4.5 9.4 1.0
CB X:ASN297 4.6 9.7 1.0
OE1 X:GLU130 4.6 11.5 1.0
CA X:GLY296 4.6 9.7 1.0
N X:ASN297 4.7 9.4 1.0
N X:TRP299 4.7 9.6 1.0
CB X:ASN293 4.7 9.2 1.0
C X:ASN297 4.7 10.5 1.0
CA X:ASN293 4.8 9.6 1.0
CA X:ASN297 4.8 10.1 1.0
C X:TRP299 4.9 9.5 1.0
CA X:TRP299 5.0 10.0 1.0
CB X:GLU300 5.0 10.0 1.0
CB X:ALA298 5.0 10.0 1.0

Strontium binding site 2 out of 2 in 1y1h

Go back to Strontium Binding Sites List in 1y1h
Strontium binding site 2 out of 2 in the Human Formylglycine Generating Enzyme, Oxidised Cys Refined As Hydroperoxide


Mono view


Stereo pair view

A full contact list of Strontium with other atoms in the Sr binding site number 2 of Human Formylglycine Generating Enzyme, Oxidised Cys Refined As Hydroperoxide within 5.0Å range:
probe atom residue distance (Å) B Occ
X:Sr1002

b:13.2
occ:1.00
O X:ILE260 2.4 11.2 1.0
O X:HOH2026 2.4 13.7 1.0
OD1 X:ASN259 2.4 9.6 1.0
O X:PHE275 2.5 11.9 1.0
OD2 X:ASP273 2.5 11.1 1.0
O X:HOH2020 2.6 13.0 1.0
OD1 X:ASP273 2.6 10.6 1.0
CG X:ASP273 2.9 12.2 1.0
C X:ILE260 3.6 11.4 1.0
C X:PHE275 3.7 11.9 1.0
CG X:ASN259 3.7 10.2 1.0
OE1 X:GLN262 3.9 13.4 1.0
N X:ILE260 3.9 10.2 1.0
C X:ASN259 4.3 9.2 1.0
CB X:ASP273 4.4 12.5 1.0
CA X:ILE260 4.4 10.6 1.0
NE2 X:GLN262 4.4 10.8 1.0
CA X:PHE275 4.4 11.6 1.0
CA X:ASN259 4.4 9.5 1.0
N X:PHE275 4.5 11.6 1.0
CD X:GLN262 4.5 11.8 1.0
CB X:PHE275 4.5 11.7 1.0
N X:TRP261 4.6 12.0 1.0
ND2 X:ASN259 4.6 10.1 1.0
O X:TYR334 4.6 12.1 1.0
O X:GLN276 4.6 12.7 1.0
N X:GLN276 4.6 12.1 1.0
CA X:TRP261 4.6 12.1 1.0
CB X:ASN259 4.6 9.3 1.0
OD1 X:ASN269 4.7 19.6 1.0
ND2 X:ASN269 4.7 14.2 1.0
CA X:GLN276 4.8 13.1 1.0
C X:GLN276 4.9 12.2 1.0
O X:GLY277 5.0 11.4 1.0

Reference:

T.Dierks, A.Dickmanns, A.Preusser-Kunze, B.Schmidt, M.Mariappan, K.Von Figura, R.Ficner, M.G.Rudolph. Molecular Basis For Multiple Sulfatase Deficiency and Mechanism For Formylglycine Generation of the Human Formylglycine-Generating Enzyme. Cell(Cambridge,Mass.) V. 121 541 2005.
ISSN: ISSN 0092-8674
PubMed: 15907468
DOI: 10.1016/J.CELL.2005.03.001
Page generated: Mon Jan 25 16:03:09 2021

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